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Urban food is a key lever for transformative change towards sustainability. While research reporting on the urban food practices (UFPs) in support of sustainability is increasing, the link towards transformative potential is lacking. This is because research on urban food is often place-based and contextual. This limits the applicability of insights to large-scale sustainability transformations. This paper describes UFPs that aim to contribute to transformative change. We present signposts for potential change based on the types of intended transformative changes as described in the reviewed literature based on the processes and outcomes of the urban food policies and programmes. Secondly, we classify diverse UFPs to elevate them beyond their local, place-based contexts. We find that UFPs carry a lot of potential to facilitate sustainability transformations. Based on that analysis, we provide insights on how urban food research can further contribute to harnessing the transformative potential of UFPs for actionable purposes.

Bacterial nitric oxide reductases (NORs) catalyse the reduction of NO to N2O and H2O. NORs are found either in denitrification chains, or in pathogens where their primary role is detoxification of NO produced by the immune defense of the host. Although NORs belong to the heme-copper oxidase superfamily, comprising proton-pumping O-2-reducing enzymes, the best studied NORs, cNORs (cytochrome c-dependent), are non-electrogenic. Here, we focus on another type of NOR, qNOR (quinol-dependent). Recombinant qNOR from Neisseria meningitidis, a human pathogen, purified from Escherichia coli, showed high catalytic activity and spectroscopic properties largely similar to cNORs. However, in contrast to cNOR, liposome-reconstituted qNOR showed respiratory control ratios above two, indicating that NO reduction by qNOR was electrogenic. Further, we determined a 4.5 angstrom crystal structure of the N. meningitidis qNOR, allowing exploration of a potential proton transfer pathway from the cytoplasm by mutagenesis. Most mutations had little effect on the activity, however the E-498 variants were largely inactive, while the corresponding substitution in cNOR was previously shown not to induce significant effects. We thus suggest that, contrary to cNOR, the N. meningitidis qNOR uses cytoplasmic protons for NO reduction. Our results allow possible routes for protons to be discussed.

Superoxide dismutase-1 (SOD1) mutants, including those with unaltered enzymatic activity, are known to cause amyotrophic lateral sclerosis (ALS). Several destabilizing factors contribute to pathogenicity including a reduced ability to complete the normal maturation process which comprises folding, metal cofactor acquisition, intra-subunit disulphide bond formation and dimerization. Immature SOD1 forms toxic oligomers and characteristic large insoluble aggregates within motor system cells. Here we report that the cysteine-reactive molecule ebselen efficiently confers the SOD1 intra-subunit disulphide and directs correct SOD1 folding, depopulating the globally unfolded precursor associated with aggregation and toxicity. Assisted formation of the unusual SOD1 cytosolic disulphide bond could have potential therapeutic applications. In less reducing environments, ebselen forms a selenylsulphide with Cys111 and restores the monomer-dimer equilibrium of A4V SOD1 to wild-type. Ebselen is therefore a potent bifunctional pharmacological chaperone for SOD1 that combines properties of the SOD1 chaperone hCCS and the recently licenced antioxidant drug, edaravone.

Background: Mesocosm experiments have become increasingly popular in climate change research as they bridge the gap between small-scale, less realistic, microcosm experiments, and large-scale, more complex, natural systems. Characteristics of aquatic mesocosm designs (e.g., mesocosm volume, study duration, and replication) vary widely, potentially affecting the magnitude and direction of effect sizes measured in experiments. In this global systematic review we aim to identify the type, direction and strength of climate warming effects on aquatic species, communities and ecosystems in mesocosm experiments. Furthermore, we will investigate the context-dependency of the observed effects on several a priori determined effect moderators (ecological and methodological). Our conclusions will provide recommendations for aquatic scientists designing mesocosm experiments, as well as guidelines for interpretation of experimental results by scientists, policy-makers and the general public. Methods: We will conduct a systematic search using multiple online databases to gather evidence from the scientific literature on the effects of warming experimentally tested in aquatic mesocosms. Data from relevant studies will be extracted and used in a random effects meta-analysis to estimate the overall effect sizes of warming experiments on species performance, biodiversity and ecosystem functions. Experimental characteristics (e.g., mesocosm size and shape, replication-level, experimental duration and design, biogeographic region, community type, crossed manipulation) will be further analysed using subgroup analyses.

A new coarse-grained model of the E. coli cytoplasm is developed by describing the proteins of the cytoplasm as flexible units consisting of one or more spheres that follow Brownian dynamics (BD), with hydrodynamic interactions (HI) accounted for by a mean

The genus Leptolyngbya comprises filamentous cyanobacteria that are important in rice fields. In the rhizosphere, cyanobacteria produce a variety of secondary metabolites such as auxins that are important in agriculture soil performance. To assess this, Leptolyngbya strain MMG-1, was isolated from the rhizosphere of rice plants and described. For this, the morphology of this strain was studied by light microscopy as well as by confocal laser scanning microscopy. Besides, the ability of this strain to synthesize an auxin-like bioactive compound was demonstrated under various culture conditions (different amounts of tryptophan; pH; different alternating light:dark periods; duration of the incubation). The auxin-like compound was extracted from the culture of Leptolyngbya strain MMG-1 and identified as indole-3-acetic acid (IAA) by thin layer chromatography (TLC) as well as by high performance liquid chromatography (HPLC). Our results showed that the strain required the precursor L-tryptophan for the synthesis of IAA. Leptolyngbya strain MMG-1 accumulated IAA intracellularly. The IAA secreted by Leptolyngbya strain MMG-1 was significantly correlated with the initial concentration of L-tryptophan in the medium, as well as with the duration of the incubation. The bioactivity of the secreted IAA was determined by its effect on the rooting pattern of Pisum sativum seedlings. The culture supernatant of Leptolyngbya strain MMG-1 stimulated the seedling lateral rooting, while it decreased root length. Hence, rhizospheric Leptolyngbya produced auxin under different conditions and affected the plants rooting pattern.

Microorganisms that live in the rhizosphere play a pivotal role in the functioning and maintenance of soil ecosystems. The study of rhizospheric cyanobacteria has been hampered by the difficulty to culture and maintain them in the laboratory. The present work investigated the production of the plant hormone indole-3-acetic acid (IAA) and the potential of biofilm formation on the rhizoplane of pea plants by two cyanobacterial strains, isolated from rice rhizosphere. The unicellular cyanobacteria Chroococcidiopsis sp. MMG-5 and Synechocystis sp. MMG-8 that were isolated from a rice rhizosphere, were investigated. Production of IAA by Chroococcidiopsis sp. MMG-5 and Synechocystis sp. MMG-8 was measured under experimental conditions (pH and light). The bioactivity of the cyanobacterial auxin was demonstrated through the alteration of the rooting pattern of Pisum sativum seedlings. The increase in the concentration of L-tryptophan and the time that this amino acid was present in the medium resulted in a significant enhancement of the synthesis of IAA (r > 0.900 at p = 0.01). There was also a significant correlation between the concentration of IAA in the supernatant of the cyanobacteria cultures and the root length and number of the pea seedlings. Observations made by confocal laser scanning microscopy revealed the presence of cyanobacteria on the surface of the roots and also provided evidence for the penetration of the cyanobacteria in the endorhizosphere. We show that the synthesis of IAA by Chroococcidiopsis sp. MMG-5 and Synechocystis sp. MMG-8 occurs under different environmental conditions and that the auxin is important for the development of the seedling roots and for establishing an intimate symbiosis between cyanobacteria and host plants.

Arthrospira platensis is a cyanobacterium known for its nutritional value and secondary metabolites. Extracellular polymeric substances (EPS) are an important trait of most cyanobacteria, including A. platensis. Here, we extracted and analysed different fractions of EPS from a locally isolated strain of A. platensis. Three different fractions of EPS were distinguished. These were EPS released into the medium (REPS), EPS loosely bound to the organism (LEPS) and EPS tightly bound to the organism (TEPS), which were extracted by different procedures. The LEPS fraction was smaller than the other two fractions. The EPS of A. platensis exhibited high diversity. Total protein and carbohydrate content was determined in each of these fractions. The largest amount of total carbohydrates and total proteins was in the TEPS fraction. Eight sugar moieties were detected and analysed in all EPS fractions using HPAE-PAD. Fructose, mannose and ribose were rare sugar residues in all fractions of EPS. With the exception of fructose, all sugars tested for were detected in TEPS. The amount of sugars detected was significantly higher in TEPS compared with the two other fractions, especially for galactose, xylose and glucose. The EPS were localized by confocal laser scanning microscopy (CLSM) after staining with different fluorescent dyes and it was found that A. platensis possessed a thick and smooth layer of EPS around the spiral trichomes.

A variety of microscopic techniques have been utilized to study cyanobacterial associations with plant roots, but confocal laser scanning microscopy (CLSM) is the least used due to the unavailability of a suitable fluorescent dye. Commonly used lectins have problems with their binding ability with root cells and their visualization under CLSM. DTAF (5-(4,6-dichlorotriazinyl) aminofluorescein) is a fluorescent dye that has been widely used for staining various biological samples for fluorescent microscopy. It reacts with polysaccharides and peptides at ordinary conditions. The possible application and efficiency of DTAF for CLSM studies were examined in various aspects of cyanobacterial-plant interactions. Seedlings of Pisum sativum, Vigna rediata and Triticum aestivum were co-cultivated and stained with DTAF as a fluorochrome. Extracellular and intracellular interactions of cyanobacteria and the plant root surface were observed by CLSM. Results were compared with staining by other commonly used lectins. Advantages of the use of DTAF over other stains are its penetration into root tissues and binding with polysaccharides, mainly the cellulose. The staining was smooth, which clearly showed minute details on the cell of surface and root hairs with higher resolution. The emission wavelength for DTAF is 517 nm, which is highly advantageous as cyanobacteria have auto-fluorescence at 665 nm, and both can be simultaneously used in CLSM by visualizing in different channels. This worked efficiently with all three plants used and with filamentous and unicellular cyanobacterial strains. Cyanobacterial presence was not only clearly observed on the root surface, but also inside the root tissue and epidermal cells. The easy protocol and absence of tissue processing make DTAF a useful probe for studies of cyanobacterial associations with plant roots by CLSM., A variety of microscopic techniques have been utilized to study cyanobacterial associations with plant roots, but confocal laser scanning microscopy (CLSM) is the least used due to the unavailability of a suitable fluorescent dye. Commonly used lectins have problems with their binding ability with root cells and their visualization under CLSM. DTAF (5-(4,6-dichlorotriazinyl) aminofluorescein) is a fluorescent dye that has been widely used for staining various biological samples for fluorescent microscopy. It reacts with polysaccharides and peptides at ordinary conditions. The possible application and efficiency of DTAF for CLSM studies were examined in various aspects of cyanobacterial-plant interactions. Seedlings of Pisum sativum, Vigna rediata and Triticum aestivum were co-cultivated and stained with DTAF as a fluorochrome. Extracellular and intracellular interactions of cyanobacteria and the plant root surface were observed by CLSM. Results were compared with staining by other commonly used lectins. Advantages of the use of DTAF over other stains are its penetration into root tissues and binding with polysaccharides, mainly the cellulose. The staining was smooth, which clearly showed minute details on the cell of surface and root hairs with higher resolution. The emission wavelength for DTAF is 517 nm, which is highly advantageous as cyanobacteria have auto-fluorescence at 665 nm, and both can be simultaneously used in CLSM by visualizing in different channels. This worked efficiently with all three plants used and with filamentous and unicellular cyanobacterial strains. Cyanobacterial presence was not only clearly observed on the root surface, but also inside the root tissue and epidermal cells. The easy protocol and absence of tissue processing make DTAF a useful probe for studies of cyanobacterial associations with plant roots by CLSM.

The filamentous cyanobacterium Arthrospira platensis strain MMG-9 was isolated from a rice field. The ability of this strain to synthesize the bioactive compound indole- 3-acetic acid (IAA) was demonstrated. IAA was extracted from the culture of A. platensis strain MMG-9 and its identity was confirmed by thin-layer chromatography (TLC) as well as by high- erformance liquid chromatography (HPLC). The IAA precursor L-tryptophan was required for IAA biosynthesis. Released IAA increased with the increase of the initial concentration of L-tryptophan in the medium and with the incubation time. A. platensis strain MMG-9 accumulated more IAA than it released into the medium. The bioactivity of the secreted IAA was shown by its effect on the formation of roots by Pisum sativum. There was a significant positive effect of the supernatant of cultures of A. platensis strain MMG-9 on the number of lateral roots of P. sativum, whereas a negative effect on root length was observed., The filamentous cyanobacterium Arthrospira platensis strain MMG-9 was isolated from a rice field. The ability of this strain to synthesize the bioactive compound indole- 3-acetic acid (IAA) was demonstrated. IAA was extracted from the culture of A. platensis strain MMG-9 and its identity was confirmed by thin-layer chromatography (TLC) as well as by high- erformance liquid chromatography (HPLC). The IAA precursor L-tryptophan was required for IAA biosynthesis. Released IAA increased with the increase of the initial concentration of L-tryptophan in the medium and with the incubation time. A. platensis strain MMG-9 accumulated more IAA than it released into the medium. The bioactivity of the secreted IAA was shown by its effect on the formation of roots by Pisum sativum. There was a significant positive effect of the supernatant of cultures of A. platensis strain MMG-9 on the number of lateral roots of P. sativum, whereas a negative effect on root length was observed.

Cyanobacteria have the ability to form associations with organisms from all domains of life, notably with plants, which they provide with fixed nitrogen, among other substances. This study was aimed at developing artificial associations between nonheterocystous cyanobacteria and selected crop plants. We isolated several non-heterocystous cyanobacteria from various rice fields. The cultures were tested for their capacity to produce the plant hormone indole-3- acetic acid (IAA), and the possible role of IAA in the association of cyanobacteria with seedling roots was evaluated. Axenic cultures were co-inoculated with 10-day-old plant seedlings of Triticum aestivum, Vigna radiata and Pisum sativum and incubated for 1 week. Cyanobacterial association with the roots of these seedlings was quantified by measuring chlorophyll-a. Cyanobacterial associ by light microscopy as well as by confocal laser scanning microscopy (CLSM). Based on sequence analysis of the 16S rRNA gene, the isolates were identified as Synechocystis sp., Chroococcidiopsis sp., Leptolyngbya sp., and Phormidium sp. CLSM observations revealed the intimate association of cyanobacteria with the seedling roots as well as invasion of the roots and root cells. Strains producing IAA were more efficient in the colonization of the roots than those that lacked this ability. IAA-produ a tryptophan-dependent pathway, and these cyanobacteria showed IAA synthesis activity in the presence of roots in media lacking tryptophan. Based on the results of this study, we conclude that nonheterocystous cyanobacteria also have the potential for use in agriculture to improve the growth and yield of crop plants that do not naturally form associations with cyanobacteria, Cyanobacteria have the ability to form associations with organisms from all domains of life, notably with plants, which they provide with fixed nitrogen, among other substances. This study was aimed at developing artificial associations between nonheterocystous cyanobacteria and selected crop plants. We isolated several non-heterocystous cyanobacteria from various rice fields. The cultures were tested for their capacity to produce the plant hormone indole-3- acetic acid (IAA), and the possible role of IAA in the association of cyanobacteria with seedling roots was evaluated. Axenic cultures were co-inoculated with 10-day-old plant seedlings of Triticum aestivum, Vigna radiata and Pisum sativum and incubated for 1 week. Cyanobacterial association with the roots of these seedlings was quantified by measuring chlorophyll-a. Cyanobacterial associ by light microscopy as well as by confocal laser scanning microscopy (CLSM). Based on sequence analysis of the 16S rRNA gene, the isolates were identified as Synechocystis sp., Chroococcidiopsis sp., Leptolyngbya sp., and Phormidium sp. CLSM observations revealed the intimate association of cyanobacteria with the seedling roots as well as invasion of the roots and root cells. Strains producing IAA were more efficient in the colonization of the roots than those that lacked this ability. IAA-produ a tryptophan-dependent pathway, and these cyanobacteria showed IAA synthesis activity in the presence of roots in media lacking tryptophan. Based on the results of this study, we conclude that nonheterocystous cyanobacteria also have the potential for use in agriculture to improve the growth and yield of crop plants that do not naturally form associations with cyanobacteria

Extracellular superoxide dismutase (SOD3) is a homotetrameric copper- and zinc-containing glycoprotein with affinity for heparin. The level of SOD3 is particularly high in blood vessel walls and in the lungs. The enzyme has multiple roles including protection of the lungs against hyperoxia and preservation of nitric oxide. The common mutation R213G, which reduces the heparin affinity of SOD3, is associated with increased risk of myocardial infarctions and stroke. We report the first crystal structure of human SOD3 at 1.7 A resolution. The overall subunit fold and the subunit-subunit interface of the SOD3 dimer are similar to the corresponding structures in Cu-Zn SOD (SOD1). The metal-binding sites are similar to those found in SOD1, but with Asn180 replacing Thr137 at the Cu-binding site and a much shorter loop at the zinc-binding site. The dimers form a functional homotetramer that is fashioned through contacts between two extended loops on each subunit. The N- and C-terminal end regions required for tetramerisation and heparin binding, respectively, are highly flexible. Two grooves fashioned by the tetramer interface are suggestive as the probable sites for heparin and collagen binding.

Cyanobacteria are very sociable organisms having ability to form symbiotic relationships with a variety of organisms from all other domains of life. Their association with plants is of prime importance. Very less work is done on development of new artificial symbiotic associations between cyanobacteria and crops of agricultural importance. Present study deals with formation of association between cyanobacteria, from different taxonomic classes and different economically important crops. Cyanobacteria, mainly isolated from rice fields were used. These cyanobacteria were co-inoculated with ten days old seedlings for one week. Roots were observed by light microscopy, fluorescent microscopy and confocal laser scanning microscope (CLSM) to locate the presence of cyanobacteria in roots. Chlorophyll-a content from the roots was estimated to quantify the extent of cyanobacterial association with roots. Extracellular polysaccharides (EPS) from cyanobacteria was extracted and characterized for comparison, to find component actively involved in the formation of association. Indole-3-acetic acid was determined in media to view its role in colonization. Cyanobacterial strains were identified by ribotyping. Isolated cyanobacteria were both unicellular and filamentous, Identified as Synechocystis sp., Chroococcidiopsis sp., Oscillatoria sp., Phormidium sp. and Arthrospira sp. on the basis of 16S rRNA. Filamentous cyanobacteria showed significantly more attachment with roots and prefer the entire root. Root tips were not invaded in beginning but in later stages cyanobacterial growth was also present on tips. Unicellular strains were entangled in root hairs in beginning and in later stages colonize the rhizoplane also. After ten days cyanobacteria were also present inside the roots. Cyano-plant association is initiated by EPS, produced by cyanobacteria and strength of attachment depends on extent of cyanobacterial EPS released. It was observed that attachment of cyanobacteria to roo, Cyanobacteria are very sociable organisms having ability to form symbiotic relationships with a variety of organisms from all other domains of life. Their association with plants is of prime importance. Very less work is done on development of new artificial symbiotic associations between cyanobacteria and crops of agricultural importance. Present study deals with formation of association between cyanobacteria, from different taxonomic classes and different economically important crops. Cyanobacteria, mainly isolated from rice fields were used. These cyanobacteria were co-inoculated with ten days old seedlings for one week. Roots were observed by light microscopy, fluorescent microscopy and confocal laser scanning microscope (CLSM) to locate the presence of cyanobacteria in roots. Chlorophyll-a content from the roots was estimated to quantify the extent of cyanobacterial association with roots. Extracellular polysaccharides (EPS) from cyanobacteria was extracted and characterized for comparison, to find component actively involved in the formation of association. Indole-3-acetic acid was determined in media to view its role in colonization. Cyanobacterial strains were identified by ribotyping. Isolated cyanobacteria were both unicellular and filamentous, Identified as Synechocystis sp., Chroococcidiopsis sp., Oscillatoria sp., Phormidium sp. and Arthrospira sp. on the basis of 16S rRNA. Filamentous cyanobacteria showed significantly more attachment with roots and prefer the entire root. Root tips were not invaded in beginning but in later stages cyanobacterial growth was also present on tips. Unicellular strains were entangled in root hairs in beginning and in later stages colonize the rhizoplane also. After ten days cyanobacteria were also present inside the roots. Cyano-plant association is initiated by EPS, produced by cyanobacteria and strength of attachment depends on extent of cyanobacterial EPS released. It was observed that attachment of cyanobacteria to roo

Bacterial nitric oxide reductases (NORs) catalyse the reduction of two NO to N2O and H2O. NORs are found either in denitrification chains, or in pathogens where their primary role is detoxification of NO produced by the host. Although NORs are members of the heme-copper oxidase superfamily, and thus relatives of proton-pumping O2-reducing enzymes, the best studied NORs, cNORs (cytochrome c dependent), were found to be non-electrogenic. Here, we focus on another type of NOR, qNOR (quinol-dependent). qNOR from Neisseria meningitidis, a human pathogen, was expressed in Escherichia coli and purified as a stable and highly active NO reductase. Spectroscopic and metal analysis of the purified qNOR showed properties largely similar to those in cNORs. Furthermore, the liposome-reconstituted qNOR showed respiratory control ratios consistently above 2, indicative of an electrogenic reaction. We also exchanged residues in a putative proton pathway leading from the cytoplasm to the active site, but there were no significant effects on either turnover rates or electrogenicity. However, the exchange of a glutamate close to the active site (E-498) yielded drastic effects on turnover. We thus suggest that the N. meningitidis qNOR uses cytoplasmic protons, but that the pathway is rather wide and redundant, narrowing around the glutamate-498.